2-44320435-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_000341.4(SLC3A1):āc.1854G>Cā(p.Met618Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,613,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in Lovd.
Frequency
Consequence
NM_000341.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC3A1 | NM_000341.4 | c.1854G>C | p.Met618Ile | missense_variant | Exon 10 of 10 | ENST00000260649.11 | NP_000332.2 | |
PREPL | NM_001171613.2 | c.*921C>G | 3_prime_UTR_variant | Exon 14 of 14 | ENST00000409411.6 | NP_001165084.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC3A1 | ENST00000260649.11 | c.1854G>C | p.Met618Ile | missense_variant | Exon 10 of 10 | 1 | NM_000341.4 | ENSP00000260649.6 | ||
PREPL | ENST00000409411 | c.*921C>G | 3_prime_UTR_variant | Exon 14 of 14 | 1 | NM_001171613.2 | ENSP00000387095.2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249352Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134918
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1461752Hom.: 0 Cov.: 50 AF XY: 0.0000468 AC XY: 34AN XY: 727196
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74232
ClinVar
Submissions by phenotype
Cystinuria Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at